Singularity/Apptainer¶

We support Singularity/Apptainer containers as an alternative way to bring your scientific application to LUMI instead of installing it using EasyBuild or Spack.

If you are familiar with Docker containers, Singularity/Apptainer containers are essentially the same thing, but are better suited for multi-user HPC systems such as LUMI. The main benefit of using a container is that it provides an isolated software environment for each application, which makes it easier to install and manage complex applications.

This page provides guidance on preparing your Singularity/Apptainer containers for use with LUMI. Please consult the container jobs page for guidance on running your container on LUMI.

Note

There are two major providers of the singularity runtime, namely Singularity CE and Apptainer, with the latter being a fork of the former. For most cases, these should be fully compatible. LUMI provides a Singularity CE runtime.

Pulling container images from a registry¶

Singularity allows pulling existing container images (Singularity or Docker) from container registries such as DockerHub or AMD Infinity Hub. Pulling container images from registries can be done on LUMI. For instance, the Ubuntu image ubuntu:22.04 can be pulled from DockerHub with the following command:

$ singularity pull docker://ubuntu:22.04

This will create the Singularity image file ubuntu_22.04.sif in the directory where the command was run. Once the image has been pulled, the container can be run. Instructions for running the container may be found on the container jobs page.

Take care when pulling container images

Please take care to only use images uploaded from reputable sources as these images can easily be a source of security vulnerabilities or even contain malicious code.

Set cache directories when using Docker containers

When pulling or building from Docker containers using singularity, the conversion can be quite heavy. Speed up the conversion and avoid leaving behind temporary files by using the in-memory filesystem on /tmp as the Singularity cache directory, i.e.

$ mkdir -p /tmp/$USER
$ export SINGULARITY_TMPDIR=/tmp/$USER
$ export SINGULARITY_CACHEDIR=/tmp/$USER

Building Apptainer/Singularity SIF containers¶

Building your own container on LUMI is, unfortunately, not in general possible. The singularity build command, in general, requires some level of root privileges, e.g. sudo or fakeroot, which are disabled on LUMI for security reasons. Thus, to build your own Singularity/Apptainer container for LUMI, you have two options:

Use the cotainr tool to build containers on LUMI (only for certain use cases).
Build your own container on your local hardware, e.g. your laptop.

Building containers using the cotainr tool¶

Cotainr is a tool that makes it easy to build Singularity/Apptainer containers on LUMI for certain use cases. It is not a general purpose container building tool.

On LUMI, cotainr is available in the LUMI central software stack and may be loaded using

$ module load LUMI
$ module load cotainr

When building containers using cotainr build, you may either specify a base image for the container yourself (using the --base-image option) or you may use the --system option to use the recommended base images for LUMI. To list the available systems, run

$ cotainr info
...

System info
-------------------------------------------------------------------------------
Available system configurations:
    - lumi-g
    - lumi-c

As an example, you may then use cotainr build to create a container for LUMI-G containing a Conda/pip environment by running

$ cotainr build my_container.sif --system=lumi-g --conda-env=my_conda_env.yml

where my_conda_env.yml is a file containing an exported Conda environment. The resulting my_container.sif container may be run like any other container job on LUMI. For example:

$ srun --partition=<partition> --account=<account> singularity exec my_container.sif python3 my_script.py

where my_script.py is your Python script.

The installed Conda environment is automatically activated when you run the container. See the cotainr Conda environment docs and the cotainr LUMI examples for more details.

Make sure your Conda environment supports the hardware in LUMI

To take advantage of e.g. the GPUs in LUMI-G, the packages you specify in your Conda environment must be compatible with LUMI-G, i.e. built against ROCm. Similarly, to take full advantage of the Slingshot 11 interconnect when running MPI jobs, you must make sure your packages are built against Cray MPICH. Cotainr does not do any magic conversion of the packages specified in the Conda environment to make sure they fit the hardware of LUMI. It simply installs the packages exactly as listed in the my_conda_env.yml file.

Note

Using cotainr to build a container from a Conda/pip environment is different from wrapping a Conda/pip environment using the LUMI container wrapper. Each serves their own purpose. See the Python installation guide for an overview of differences and this GitHub issue for a detailed discussion of the differences.

See the cotainr documentation for more details about cotainr.

Building containers on local hardware¶

You may also build a Singularity/Apptainer container for LUMI on your local hardware and transfer it to LUMI.

As an example, consider building a container that is compatible with the MPI stack on LUMI.

Warning

For MPI-enabled containers, the application inside the container must be dynamically linked to an MPI version that is ABI-compatible with the host MPI.

The following Singularity definition file mpi_osu.def, installs MPICH-3.1.4, which is ABI-compatible with the Cray-MPICH found on LUMI. That MPICH will be used to compile the OSU micro-benchmarks. Finally, the OSU point to point bandwidth test is set as the "runscript" of the image.

bootstrap: docker
from: ubuntu:21.04

%post
    # Install software
    apt-get update
    apt-get install -y file g++ gcc gfortran make gdb strace wget ca-certificates --no-install-recommends

    # Install mpich
    wget -q http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz
    tar xf mpich-3.1.4.tar.gz
    cd mpich-3.1.4
    ./configure --disable-fortran --enable-fast=all,O3 --prefix=/usr
    make -j$(nproc)
    make install
    ldconfig

    # Build osu benchmarks
    wget -q http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.2.tar.gz
    tar xf osu-micro-benchmarks-5.3.2.tar.gz
    cd osu-micro-benchmarks-5.3.2
    ./configure --prefix=/usr/local CC=$(which mpicc) CFLAGS=-O3
    make
    make install
    cd ..
    rm -rf osu-micro-benchmarks-5.3.2
    rm osu-micro-benchmarks-5.3.2.tar.gz

%runscript
    /usr/local/libexec/osu-micro-benchmarks/mpi/pt2pt/osu_bw

The image can be built on your local hardware (not on LUMI) with

$ sudo singularity build mpi_osu.sif mpi_osu.def

The mpi_osu.sif file must then be transferred to LUMI. See the container jobs MPI documentation page for instructions on running this MPI container on LUMI.